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Coexpression cluster:C4179: Difference between revisions

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|tf_chipseq_enrich=TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630267227070785
|tf_chipseq_enrich=TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630267227070785
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}}
}}

Revision as of 16:35, 26 November 2012


Full id: C4179_pineal_cerebellum_adrenal_gastric_kidney_seminal_duodenum



Phase1 CAGE Peaks

Hg19::chr2:213403880..213403914,-p1@ERBB4
Hg19::chr2:213403969..213403990,-p4@ERBB4
Hg19::chr2:213403991..213404019,-p5@ERBB4


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.63e-55114
neural tube1.68e-4756
neural rod1.68e-4756
future spinal cord1.68e-4756
neural keel1.68e-4756
regional part of nervous system1.14e-4453
regional part of brain1.14e-4453
central nervous system1.38e-4081
neural plate1.59e-4082
presumptive neural plate1.59e-4082
neurectoderm4.43e-4086
regional part of forebrain4.57e-3841
forebrain4.57e-3841
anterior neural tube4.57e-3841
future forebrain4.57e-3841
brain5.75e-3868
future brain5.75e-3868
nervous system8.65e-3889
ecto-epithelium5.71e-32104
brain grey matter1.67e-3134
gray matter1.67e-3134
telencephalon2.27e-3134
regional part of telencephalon1.32e-2932
cerebral hemisphere1.54e-2932
pre-chordal neural plate7.14e-2961
structure with developmental contribution from neural crest8.92e-28132
ectoderm-derived structure6.27e-27171
ectoderm6.27e-27171
presumptive ectoderm6.27e-27171
cerebral cortex8.97e-2325
pallium8.97e-2325
regional part of cerebral cortex5.36e-2222
neocortex3.72e-2020
anatomical cluster2.67e-17373
organ system subdivision5.57e-17223
tube6.00e-16192
anatomical conduit8.81e-15240
multi-tissue structure5.57e-14342
organ part1.16e-13218
posterior neural tube1.65e-1015
chordal neural plate1.65e-1015
organ2.95e-10503
basal ganglion3.44e-109
nuclear complex of neuraxis3.44e-109
aggregate regional part of brain3.44e-109
collection of basal ganglia3.44e-109
cerebral subcortex3.44e-109
neural nucleus3.78e-109
nucleus of brain3.78e-109
epithelium6.80e-10306
multi-cellular organism1.31e-09656
cell layer1.63e-09309
embryo1.89e-09592
telencephalic nucleus2.58e-087
developing anatomical structure4.25e-08581
diencephalon4.97e-087
future diencephalon4.97e-087
segmental subdivision of hindbrain5.62e-0812
hindbrain5.62e-0812
presumptive hindbrain5.62e-0812
cavitated compound organ1.09e-0731
temporal lobe1.37e-076
compound organ2.22e-0768
brainstem3.90e-076
segmental subdivision of nervous system4.10e-0713
gyrus7.01e-076


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
TCF12#6938310.63446490218640.0008313523990202070.00630267227070785



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.